public class Model
extends java.lang.Object
Modifier and Type | Field and Description |
---|---|
int |
act |
int |
altLocCount |
protected java.util.Map<java.lang.String,java.lang.Object> |
auxiliaryInfo |
SymmetryInterface |
biosymmetry |
(package private) int |
biosymmetryCount |
private int |
bondCount |
BS |
bsAtoms |
BS |
bsAtomsDeleted |
protected int |
chainCount |
Chain[] |
chains |
(package private) java.util.Map<java.lang.String,java.lang.Integer> |
dataFrames |
(package private) int |
dataSourceFrame |
(package private) float |
defaultRotationRadius |
java.util.Map<java.lang.String,java.lang.Object> |
dssrCache |
(package private) int |
fileIndex |
int |
firstAtomIndex |
(package private) int |
firstMoleculeIndex |
long |
frameDelay |
int |
groupCount |
protected boolean |
hasRasmolHBonds |
int |
hydrogenCount |
(package private) int |
insertionCount |
boolean |
isBioModel |
boolean |
isJmolDataFrame |
boolean |
isModelKit |
boolean |
isPdbWithMultipleBonds |
(package private) boolean |
isTrajectory |
(package private) java.lang.String |
jmolData |
(package private) java.lang.String |
jmolFrameType |
javajs.util.SB |
loadScript |
java.lang.String |
loadState |
int |
modelIndex |
int |
moleculeCount |
ModelSet |
ms
BE CAREFUL: FAILURE TO NULL REFERENCES TO modelSet WILL PREVENT
FINALIZATION AND CREATE A MEMORY LEAK.
|
Orientation |
orientation |
java.lang.String |
pdbID |
java.util.Properties |
properties |
int |
selectedTrajectory |
SymmetryInterface |
simpleCage |
boolean |
structureTainted |
int |
trajectoryBaseIndex |
(package private) javajs.util.P3 |
translation |
Constructor and Description |
---|
Model() |
Modifier and Type | Method and Description |
---|---|
(package private) void |
calcSelectedGroupsCount(BS bsSelected) |
void |
fixIndices(int modelIndex,
int nAtomsDeleted,
BS bsDeleted) |
protected void |
fixIndicesM(int modelIndex,
int nAtomsDeleted,
BS bsDeleted) |
boolean |
freeze() |
protected void |
freezeM() |
int |
getBondCount() |
(package private) Chain |
getChain(int chainID) |
Chain |
getChainAt(int i) |
int |
getChainCount(boolean countWater) |
int |
getGroupCount() |
int |
getTrueAtomCount()
not actually accessed -- just pointing out what it is
|
void |
resetBoundCount() |
Model |
set(ModelSet modelSet,
int modelIndex,
int trajectoryBaseIndex,
java.lang.String jmolData,
java.util.Properties properties,
java.util.Map<java.lang.String,java.lang.Object> auxiliaryInfo) |
public ModelSet ms
public int modelIndex
int fileIndex
public boolean isBioModel
public boolean isPdbWithMultipleBonds
public boolean isModelKit
public Chain[] chains
public SymmetryInterface simpleCage
public java.util.Map<java.lang.String,java.lang.Object> dssrCache
public Orientation orientation
protected java.util.Map<java.lang.String,java.lang.Object> auxiliaryInfo
public java.util.Properties properties
public SymmetryInterface biosymmetry
java.util.Map<java.lang.String,java.lang.Integer> dataFrames
javajs.util.P3 translation
int dataSourceFrame
public java.lang.String loadState
public javajs.util.SB loadScript
protected boolean hasRasmolHBonds
public boolean structureTainted
public boolean isJmolDataFrame
boolean isTrajectory
public int trajectoryBaseIndex
public int altLocCount
int insertionCount
public int act
private int bondCount
protected int chainCount
public int groupCount
public int hydrogenCount
public int moleculeCount
int biosymmetryCount
public int firstAtomIndex
int firstMoleculeIndex
public final BS bsAtoms
public final BS bsAtomsDeleted
float defaultRotationRadius
public long frameDelay
public int selectedTrajectory
java.lang.String jmolData
java.lang.String jmolFrameType
public java.lang.String pdbID
public Model set(ModelSet modelSet, int modelIndex, int trajectoryBaseIndex, java.lang.String jmolData, java.util.Properties properties, java.util.Map<java.lang.String,java.lang.Object> auxiliaryInfo)
public int getTrueAtomCount()
public void resetBoundCount()
public int getBondCount()
public int getChainCount(boolean countWater)
void calcSelectedGroupsCount(BS bsSelected)
public int getGroupCount()
public Chain getChainAt(int i)
Chain getChain(int chainID)
public void fixIndices(int modelIndex, int nAtomsDeleted, BS bsDeleted)
protected void fixIndicesM(int modelIndex, int nAtomsDeleted, BS bsDeleted)
public boolean freeze()
protected void freezeM()